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- PDB-3wyh: Structure of disulfide bond deletion mutant of ostrich egg white ... -

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Basic information

Entry
Database: PDB / ID: 3wyh
TitleStructure of disulfide bond deletion mutant of ostrich egg white lysozyme
ComponentsLysozyme g
KeywordsHYDROLASE / helices rich / Sugar Binding
Function / homology
Function and homology information


peptidoglycan catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-positive bacterium / extracellular region
Similarity search - Function
Glycoside hydrolase, family 23 / Transglycosylase SLT domain 1 / Transglycosylase SLT domain / Lysozyme - #10 / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesStruthio camelus (African ostrich)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsKawaguchi, Y. / Yoneda, K. / Araki, T.
CitationJournal: To be Published
Title: Structure of disulfide bond deletion mutant of ostrich egg white lysozyme
Authors: Kawaguchi, Y. / Yoneda, K. / Araki, T.
History
DepositionAug 28, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme g
B: Lysozyme g
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6775
Polymers41,0682
Non-polymers6093
Water4,918273
1
A: Lysozyme g
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9803
Polymers20,5341
Non-polymers4462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lysozyme g
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6972
Polymers20,5341
Non-polymers1631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.188, 64.934, 131.118
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lysozyme g / 1 / 4-beta-N-acetylmuramidase / Goose-type lysozyme


Mass: 20534.148 Da / Num. of mol.: 2 / Mutation: C4S/C18S/C29S/C60S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Struthio camelus (African ostrich) / Plasmid: pPIC9K / Production host: Komagataella pastoris GS115 (fungus) / References: UniProt: P00719, lysozyme
#2: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 50% PEG 200, 0.05M Li2SO4, 0.1M tris-HCl , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 16, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.77→50 Å / Num. all: 32647 / Num. obs: 29391 / Biso Wilson estimate: 24.3 Å2
Reflection shellHighest resolution: 1.77 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 153l

153l


Resolution: 1.77→29.1 Å / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1654 -RANDOM
Rwork0.186 ---
all-32695 --
obs-29391 89.9 %-
Displacement parametersBiso mean: 13.6 Å2
Refinement stepCycle: LAST / Resolution: 1.77→29.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2886 0 41 273 3200
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.018
X-RAY DIFFRACTIONr_angle_refined_deg1.64
X-RAY DIFFRACTIONr_chiral_restr0.11
LS refinement shellResolution: 1.77→1.82 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rwork0.21 2231
Rfree-135
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4TAM.param
X-RAY DIFFRACTION5P6G.param

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